Background Sweden introduced human papillomavirus (HPV) vaccination in 2006 via opportunistic, subsidized, catch-up, and school-based programs. Notably, genital warts (GW) are the first observable clinical outcome following HPV-6/11 infection, the strains targeted by vaccination. We aim to assess the incidence of GW in Sweden and its change throughout vaccination programs.Methods This ecological study used Swedish registers to obtain national population data and cases of GW from 2006 to 2018 in 15- to 44-year-old men and women. We used Poisson models to estimate GW incidence change after vaccination compared to a prevaccination period, stratified by age and sex, and incidence change of GW in birth cohorts eligible for vaccination compared to a prevaccination cohort. Finally, we estimated GW cases averted in each vaccinated cohort.Results The incidence of GW decreased during periods following HPV vaccination. In 2016-2018, over a decade after vaccination availability, incidence decreased by 89% (95% confidence interval [CI], 83%-93%), 73% (95% CI, 71%-75%), 50% (95% CI, 43%-56%), and 20% (95% CI, 10%-28%) in women aged 15-19, 20-24, 25-29, and 30-34 years, respectively. A similar reduction was observable in men, although of lower magnitude. We estimated 18 890 and 12 343 GW cases averted among vaccinated cohorts of women and men, respectively.Conclusions We report on population-level decreases of GW incidence in women and men following increased vaccination coverage. Cohorts eligible for school-based vaccination recorded the largest decrease in GW incidence in Sweden to date. For the period under study, decreases among men could be attributed to herd effects. HPV vaccination programs have significantly reduced incidence of genital warts in Sweden, especially among women aged 15-34 years. Incidence among men has also decreased substantially, likely through herd effect. During 2006-2018, 31 233 cases were averted, highlighting the vaccination's remarkable population-level impact.